diff --git a/.bootstrap/config/core.toml b/.bootstrap/config/core.toml
index b3ef373f..e0e8b0f7 100644
--- a/.bootstrap/config/core.toml
+++ b/.bootstrap/config/core.toml
@@ -174,10 +174,6 @@ examples = "feature_example"
 template = "prd_template"
 examples = "prd_example"
 
-[kits.sdlc.resources.skill]
-path = "config/kits/sdlc/SKILL.md"
-kind = "skill"
-
 [kits.sdlc.resources.agents]
 path = "config/kits/sdlc/AGENTS.md"
 kind = "rule"
diff --git a/skills/studio/scripts/studio/commands/agents.py b/skills/studio/scripts/studio/commands/agents.py
index 94c4be3f..55fe644f 100644
--- a/skills/studio/scripts/studio/commands/agents.py
+++ b/skills/studio/scripts/studio/commands/agents.py
@@ -1707,15 +1707,6 @@ def _default_agents_config() -> dict:
                 "skills": {
                     "custom_content": "",
                     "outputs": shared_skills + [
-                        {
-                            "path": ".github/copilot-instructions.md",
-                            "template": [
-                                "# Constructor Studio",
-                                _GENERATED_MARKER,
-                                "",
-                                "{custom_content}",
-                            ],
-                        },
                         {
                             "path": ".github/prompts/cf.prompt.md",
                             "template": [
@@ -2471,15 +2462,6 @@ def _has_non_openai_install_signal(project_root: Path) -> bool:
     if _file_has_studio_follow_link(project_root / ".cursor" / "rules" / "studio.mdc"):
         return True
 
-    legacy_ci = project_root / ".github" / "copilot-instructions.md"
-    if legacy_ci.is_file():
-        try:
-            ci_text = legacy_ci.read_text(encoding="utf-8")
-            if ci_text.startswith("# Constructor Studio") or ci_text.startswith("# Studio"):
-                return True
-        except (OSError, UnicodeDecodeError):
-            pass
-
     return (
         (project_root / ".github" / "prompts" / "cf.prompt.md").is_file()
         or (project_root / ".github" / "prompts" / "studio.prompt.md").is_file()
@@ -2597,18 +2579,8 @@ def _is_agent_installed(agent: str, project_root: Path) -> bool:
                     return True
 
     # ── Legacy Copilot fallback ───────────────────────────────────────────
-    # A Constructor Studio-managed copilot-instructions.md (starts with
-    # "# Constructor Studio" or legacy "# Studio") is a valid signal from
-    # pre-marker installs.  Also detect via prompts file.
+    # Detect via prompts files and legacy install markers only.
     if agent == "copilot":
-        legacy_ci = project_root / ".github" / "copilot-instructions.md"
-        if legacy_ci.is_file():
-            try:
-                ci_text = legacy_ci.read_text(encoding="utf-8")
-                if ci_text.startswith("# Constructor Studio") or ci_text.startswith("# Studio"):
-                    return True
-            except (OSError, UnicodeDecodeError):
-                pass
         for prompt_name in ("cf.prompt.md", "studio.prompt.md", "cypilot.prompt.md"):
             if (project_root / ".github" / "prompts" / prompt_name).is_file():
                 return True
@@ -3381,21 +3353,6 @@ def _process_skills(
             continue
         out_path, rel_path, content = rendered
 
-        # Guard: skip overwriting user-authored copilot-instructions.md.
-        # The file is only Constructor Studio-managed when it starts with "# Constructor Studio" or legacy "# Studio".
-        if rel_path == ".github/copilot-instructions.md" and out_path.is_file():
-            try:
-                existing = out_path.read_text(encoding="utf-8")
-            except OSError:
-                existing = ""
-            if not existing.startswith("# Constructor Studio") and not existing.startswith("# Studio"):
-                rel = _safe_relpath(out_path.resolve(), project_root)
-                skills_result["skipped"].append(
-                    f"{rel} (user-authored, not overwriting)"
-                )
-                skills_result["_copilot_user_authored"] = True
-                continue
-
         _write_or_skip(out_path, content, skills_result, project_root, dry_run)
 
     return skills_result
@@ -3798,6 +3755,85 @@ def _process_kit_public_agents_and_rules(
     return {"agents": public_agents, "rules": public_rules}
 
 
+def _collect_managed_result_paths(
+    project_root: Path,
+    section: Dict[str, Any],
+) -> Set[str]:
+    """Collect normalized project-relative output paths from a generator result."""
+    paths: Set[str] = set()
+    for key in ("created", "updated", "unchanged", "deleted"):
+        values = section.get(key, [])
+        if not isinstance(values, list):
+            continue
+        for value in values:
+            if isinstance(value, tuple):
+                candidates = [value[-1]]
+            else:
+                candidates = [value]
+            for candidate in candidates:
+                if not isinstance(candidate, str) or not candidate.strip():
+                    continue
+                candidate_path = Path(candidate)
+                if candidate_path.is_absolute():
+                    paths.add(_safe_relpath(candidate_path, project_root))
+                else:
+                    paths.add(candidate.replace("\\", "/").strip("/"))
+    for output in section.get("outputs", []):
+        if not isinstance(output, dict):
+            continue
+        raw_path = output.get("path")
+        if not isinstance(raw_path, str) or not raw_path.strip():
+            continue
+        candidate_path = Path(raw_path)
+        if candidate_path.is_absolute():
+            paths.add(_safe_relpath(candidate_path, project_root))
+        else:
+            paths.add(raw_path.replace("\\", "/").strip("/"))
+    return {path for path in paths if path}
+
+
+def list_managed_agent_output_paths(
+    project_root: Path,
+    studio_root: Path,
+) -> List[str]:
+    """Return exact CFS-managed agent integration paths for the current install."""
+    cfg = _default_agents_config()
+    managed_paths: Set[str] = set()
+
+    for marker_path, _marker_content in _INSTALL_MARKERS.values():
+        managed_paths.add(marker_path)
+
+    for agent in _ALL_RECOGNIZED_AGENTS:
+        agent_cfg = cfg.get("agents", {}).get(agent, {})
+        skills_cfg = agent_cfg.get("skills", {}) if isinstance(agent_cfg, dict) else {}
+        outputs = skills_cfg.get("outputs") if isinstance(skills_cfg, dict) else None
+        if isinstance(outputs, list):
+            for output in outputs:
+                if not isinstance(output, dict):
+                    continue
+                rel_path = output.get("path")
+                if isinstance(rel_path, str) and rel_path.strip():
+                    managed_paths.add(rel_path.replace("\\", "/").strip("/"))
+        sections: List[Dict[str, Any]] = []
+        sections.append(_process_workflows(agent, project_root, studio_root, cfg, None, dry_run=True))
+        sections.append(_process_skills(agent, project_root, studio_root, cfg, None, dry_run=True))
+        sections.append(_process_kit_workflow_skills(agent, project_root, studio_root, cfg, None, dry_run=True))
+        sections.append(_process_subagents(agent, project_root, studio_root, cfg, None, dry_run=True))
+        public_sections = _process_kit_public_agents_and_rules(
+            agent,
+            project_root,
+            studio_root,
+            dry_run=True,
+        )
+        sections.append(public_sections.get("agents", {}))
+        sections.append(public_sections.get("rules", {}))
+        for section in sections:
+            if isinstance(section, dict):
+                managed_paths.update(_collect_managed_result_paths(project_root, section))
+
+    return sorted(path for path in managed_paths if path)
+
+
 def _process_legacy_cleanup(
     agent: str,
     project_root: Path,
@@ -3924,9 +3960,8 @@ def _process_legacy_cleanup(
     # @cpt-begin:cpt-studio-algo-agent-integration-generate-shims:p1:inst-write-install-marker
     # Tools that share generic directories need a unique Constructor Studio-specific
     # marker so detection/regeneration can distinguish Constructor Studio installs from
-    # unrelated user files.  The marker is always created when the agent is
-    # processed — even if copilot-instructions.md was preserved as user-
-    # authored, the other generated outputs (prompts, shared skills, agents)
+    # unrelated user files. The marker is always created when the agent is
+    # processed because the other generated outputs (prompts, shared skills, agents)
     # still need to be managed by future `cfs update` runs.
     marker_info = _INSTALL_MARKERS.get(agent)
     if marker_info and not dry_run:
diff --git a/skills/studio/scripts/studio/commands/init.py b/skills/studio/scripts/studio/commands/init.py
index 33be0e4a..a60f6eba 100644
--- a/skills/studio/scripts/studio/commands/init.py
+++ b/skills/studio/scripts/studio/commands/init.py
@@ -14,6 +14,7 @@
 from ..utils.artifacts_meta import create_backup, generate_default_registry, generate_slug
 from ..utils import toml_utils
 from ..utils.ui import ui
+from .agents import list_managed_agent_output_paths
 
 # Cache-managed install content: core directories go into .core/, root files go into the install root.
 # Full directories (copied entirely)
@@ -360,6 +361,7 @@ def _ignored_kit_paths(core_toml_path: Path, default: str = "tracked") -> List[s
 
 
 def _gitignore_patterns(
+    project_root: Path,
     install_dir: str,
     ignored_kit_paths: List[str],
     runtime_tracking: str = "ignored",
@@ -373,56 +375,9 @@ def _gitignore_patterns(
             f"{install_rel}/{GEN_SUBDIR}/",
         ])
     if agent_tracking == "ignored":
-        patterns.extend([
-            ".agents/skills/cf/",
-            ".agents/skills/cf-*/",
-            ".agents/skills/studio-*/",
-            ".agents/skills/cypilot-*/",
-            ".agents/skills/cf-constructor-*/",
-            ".codex/agents/cf*.toml",
-            ".codex/agents/studio-*.toml",
-            ".codex/agents/cypilot-*.toml",
-            ".codex/agents/cf-constructor-*.toml",
-            ".codex/agents/storytelling-*.toml",
-            ".codex/.cf-installed",
-            ".codex/.constructor-studio-installed",
-            ".claude/skills/cf/",
-            ".claude/skills/cf-*/",
-            ".claude/commands/cf*.md",
-            ".claude/commands/studio-*.md",
-            ".claude/commands/cypilot-*.md",
-            ".claude/commands/cf-constructor-*.md",
-            ".claude/agents/cf*.md",
-            ".claude/agents/studio-*.md",
-            ".claude/agents/cypilot-*.md",
-            ".claude/agents/cf-constructor-*.md",
-            ".claude/agents/storytelling-*.md",
-            ".cursor/commands/cf*.md",
-            ".cursor/commands/studio-*.md",
-            ".cursor/commands/cypilot-*.md",
-            ".cursor/commands/cf-constructor-*.md",
-            ".cursor/agents/cf*.md",
-            ".cursor/agents/studio-*.md",
-            ".cursor/agents/cypilot-*.md",
-            ".cursor/agents/cf-constructor-*.md",
-            ".cursor/agents/storytelling-*.md",
-            ".github/prompts/cf*.prompt.md",
-            ".github/prompts/studio-*.prompt.md",
-            ".github/prompts/cypilot-*.prompt.md",
-            ".github/prompts/cf-constructor-*.prompt.md",
-            ".github/agents/cf*.md",
-            ".github/agents/studio-*.md",
-            ".github/agents/cypilot-*.md",
-            ".github/agents/cf-constructor-*.md",
-            ".github/agents/storytelling-*.md",
-            ".github/.cf-installed",
-            ".github/.constructor-studio-installed",
-            ".github/copilot-instructions.md",
-            ".windsurf/workflows/cf*.md",
-            ".windsurf/workflows/studio-*.md",
-            ".windsurf/workflows/cypilot-*.md",
-            ".windsurf/workflows/cf-constructor-*.md",
-        ])
+        patterns.extend(
+            list_managed_agent_output_paths(project_root, project_root / install_rel)
+        )
     for kit_path in ignored_kit_paths:
         kit_rel = kit_path.strip().replace("\\", "/").strip("/")
         if kit_rel:
@@ -431,6 +386,7 @@ def _gitignore_patterns(
 
 
 def _compute_gitignore_block(
+    project_root: Path,
     install_dir: str,
     ignored_kit_paths: List[str],
     runtime_tracking: str = "ignored",
@@ -442,6 +398,7 @@ def _compute_gitignore_block(
         "# Generated Constructor Studio runtime and agent integration files.",
         "# Files matched here are owned by Constructor Studio and may be overwritten.",
         *_gitignore_patterns(
+            project_root,
             install_dir,
             ignored_kit_paths,
             runtime_tracking=runtime_tracking,
@@ -462,6 +419,7 @@ def _write_gitignore_block(
 ) -> str:
     gitignore_path = project_root / ".gitignore"
     expected_block = _compute_gitignore_block(
+        project_root,
         install_dir,
         _ignored_kit_paths(core_toml_path, default=default_kit_tracking),
         runtime_tracking=_read_install_tracking(core_toml_path, "runtime_tracking", default="ignored"),
diff --git a/skills/studio/scripts/studio/commands/kit.py b/skills/studio/scripts/studio/commands/kit.py
index 1834b48b..7f4c4276 100644
--- a/skills/studio/scripts/studio/commands/kit.py
+++ b/skills/studio/scripts/studio/commands/kit.py
@@ -687,6 +687,7 @@ def _is_registered_kit_path_absolute(registered_kit_path: str) -> bool:
         _is_posix_absolute_path(registered_kit_path)
         or _is_windows_absolute_path(registered_kit_path)
     )
+# @cpt-end:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata-fn
 
 
 # @cpt-begin:cpt-studio-algo-kit-manifest-install:p1:inst-manifest-persist-relative-only
@@ -916,32 +917,6 @@ def _registered_slug_for_local_kit_path(
     return matches[0] if len(matches) == 1 else ""
 
 
-def _collect_kit_metadata(
-    config_kit_dir: Optional[Path],
-    kit_slug: str,
-    registered_kit_path: Optional[str] = None,
-) -> Dict[str, str]:
-    """Read installed kit files and return metadata for .gen/ aggregation.
-
-    Returns dict with:
-        agents_content — raw content of kit's AGENTS.md for ``.gen/AGENTS.md``
-    """
-    # @cpt-begin:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata
-    del kit_slug, registered_kit_path
-    result: Dict[str, str] = {"skill_nav": "", "agents_content": ""}
-
-    agents_path = config_kit_dir / _KIT_AGENTS_FILE if config_kit_dir is not None else None
-    if agents_path is not None and agents_path.is_file():
-        try:
-            result["agents_content"] = agents_path.read_text(encoding="utf-8")
-        except OSError:
-            pass
-
-    return result
-    # @cpt-end:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata
-# @cpt-end:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata-fn
-
-
 def _binding_is_public_metadata_resource(binding: Dict[str, Any], kind: str) -> bool:
     public_value = binding.get("public")
     if isinstance(public_value, bool):
@@ -951,6 +926,7 @@ def _binding_is_public_metadata_resource(binding: Dict[str, Any], kind: str) ->
     return kind in {"skill", "rule"}
 
 
+# @cpt-begin:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata
 def _collect_registered_kit_metadata(
     studio_dir: Path,
     kit_slug: str,
@@ -996,12 +972,7 @@ def _collect_registered_kit_metadata(
         except (OSError, ValueError):
             resources = {}
     if not isinstance(resources, dict) or not resources:
-        kit_dir, kit_rel_path = _resolve_registered_kit_metadata_target(
-            studio_dir,
-            kit_slug,
-            kit_entry,
-        )
-        return _collect_kit_metadata(kit_dir, kit_slug, kit_rel_path)
+        return {"skill_nav": "", "agents_content": ""}
 
     result: Dict[str, str] = {"skill_nav": "", "agents_content": ""}
     agents_parts: List[str] = []
@@ -1034,6 +1005,7 @@ def _collect_registered_kit_metadata(
                 pass
     result["agents_content"] = "\n\n".join(part for part in agents_parts if part)
     return result
+# @cpt-end:cpt-studio-algo-kit-content-mgmt:p1:inst-collect-metadata
 
 
 # ---------------------------------------------------------------------------
@@ -4240,19 +4212,23 @@ def _sync_manifest_resource_bindings(
     config_dir: Path,
     kit_slug: str,
 ) -> Optional[Dict[str, Dict[str, Any]]]:
-    """Merge existing resource bindings with any new manifest resources.
+    """Sync resource bindings to the current manifest declaration set.
 
-    Returns merged bindings dict, or None if there is no manifest.
+    Returns synced bindings dict, or None if there is no manifest.
     """
     if manifest is None:
         return None
     existing_raw = _read_kits_from_core_toml(config_dir).get(kit_slug, {}).get("resources", {})
-    merged: Dict[str, Dict[str, Any]] = {}
+    existing: Dict[str, Dict[str, Any]] = {}
     for res_id, binding in existing_raw.items():
         if isinstance(binding, dict):
-            merged[res_id] = binding
+            existing[res_id] = dict(binding)
         elif isinstance(binding, str):
-            merged[res_id] = {"path": binding}
+            existing[res_id] = {"path": binding}
+    merged: Dict[str, Dict[str, Any]] = {}
+    for res in getattr(manifest, "resources", []):
+        if getattr(res, "id", None) in existing:
+            merged[str(res.id)] = dict(existing[str(res.id)])
     kit_root_rel = _resolve_manifest_kit_root_rel(manifest, merged, kit_slug)
     for res in getattr(manifest, "resources", []):
         if res.id not in merged:
diff --git a/tests/test_agents_coverage.py b/tests/test_agents_coverage.py
index 8e23d1f0..dbcbc176 100644
--- a/tests/test_agents_coverage.py
+++ b/tests/test_agents_coverage.py
@@ -1152,7 +1152,7 @@ def test_detects_cursor_follow_link(self):
 
             self.assertTrue(_has_non_openai_install_signal(root))
 
-    def test_detects_legacy_copilot_instructions(self):
+    def test_ignores_legacy_copilot_instructions(self):
         from studio.commands.agents import _has_non_openai_install_signal
 
         with TemporaryDirectory() as tmpdir:
@@ -1161,7 +1161,7 @@ def test_detects_legacy_copilot_instructions(self):
             legacy_ci.parent.mkdir(parents=True)
             legacy_ci.write_text("# Constructor Studio\nLegacy instructions\n", encoding="utf-8")
 
-            self.assertTrue(_has_non_openai_install_signal(root))
+            self.assertFalse(_has_non_openai_install_signal(root))
 
     def test_ignores_legacy_copilot_read_errors(self):
         from studio.commands.agents import _has_non_openai_install_signal
@@ -1263,8 +1263,8 @@ def test_agents_not_configured(self):
 
         results = {
             "copilot": {
-                "workflows": {"updated": [], "created": ["/p/.github/prompts/cypilot-generate.prompt.md"]},
-                "skills": {"updated": [], "created": ["/p/.github/copilot-instructions.md"]},
+                "workflows": {"updated": [], "created": ["/p/.github/prompts/cf-generate.prompt.md"]},
+                "skills": {"updated": [], "created": ["/p/.github/prompts/cf.prompt.md"]},
             },
         }
         err = io.StringIO()
@@ -2185,8 +2185,8 @@ def test_copilot_detected_via_marker_file(self):
         from studio.commands.agents import _AGENT_MARKERS
         self.assertIn(".github/.cf-installed", _AGENT_MARKERS.get("copilot", []))
 
-    def test_copilot_generates_repo_wide_instructions(self):
-        """Copilot generation must produce .github/copilot-instructions.md (always-on)."""
+    def test_copilot_generates_prompt_entrypoint(self):
+        """Copilot generation must produce the shared prompt entrypoint and marker."""
         from studio.commands.agents import _process_single_agent, _default_agents_config
 
         with TemporaryDirectory() as td:
@@ -2201,44 +2201,14 @@ def test_copilot_generates_repo_wide_instructions(self):
             (cpt / ".core" / "workflows").mkdir(parents=True, exist_ok=True)
             cfg = _default_agents_config()
             _process_single_agent("copilot", root, cpt, cfg, None, dry_run=False)
-            instructions = root / ".github" / "copilot-instructions.md"
-            self.assertTrue(instructions.exists(), ".github/copilot-instructions.md must be generated")
-            content = instructions.read_text(encoding="utf-8")
-            self.assertNotIn("ALWAYS open and follow", content)
+            prompt = root / ".github" / "prompts" / "cf.prompt.md"
+            self.assertTrue(prompt.exists(), ".github/prompts/cf.prompt.md must be generated")
             # Marker file must also be created
             marker = root / ".github" / ".cf-installed"
             self.assertTrue(marker.exists(), ".github/.cf-installed marker must be created")
 
-    def test_copilot_cleanup_removes_legacy_skill_follow_line(self):
-        """Regeneration must clean the old generated follow-line from copilot-instructions.md."""
-        from studio.commands.agents import _process_single_agent, _default_agents_config
-
-        with TemporaryDirectory() as td:
-            root = (Path(td) / "proj").resolve()
-            root.mkdir()
-            (root / ".git").mkdir()
-            cpt = root / "cypilot"
-            cpt.mkdir()
-            core_skill = cpt / ".core" / "skills" / "studio" / "SKILL.md"
-            core_skill.parent.mkdir(parents=True)
-            core_skill.write_text("---\nname: studio\ndescription: Test\n---\nContent\n")
-            (cpt / ".core" / "workflows").mkdir(parents=True, exist_ok=True)
-
-            instructions = root / ".github" / "copilot-instructions.md"
-            instructions.parent.mkdir(parents=True, exist_ok=True)
-            instructions.write_text(
-                "# Constructor Studio\n\nALWAYS open and follow `{cf-studio-path}/.core/skills/studio/SKILL.md`\n",
-                encoding="utf-8",
-            )
-
-            cfg = _default_agents_config()
-            _process_single_agent("copilot", root, cpt, cfg, None, dry_run=False)
-
-            content = instructions.read_text(encoding="utf-8")
-            self.assertNotIn("ALWAYS open and follow", content)
-
     def test_user_authored_copilot_instructions_preserved(self):
-        """User-authored copilot-instructions.md must NOT be overwritten by generation."""
+        """User-authored copilot-instructions.md must be left untouched by generation."""
         from studio.commands.agents import _process_single_agent, _default_agents_config
 
         with TemporaryDirectory() as td:
@@ -2263,12 +2233,8 @@ def test_user_authored_copilot_instructions_preserved(self):
 
             # User content must be preserved
             self.assertEqual(instructions.read_text(encoding="utf-8"), user_content)
-            # Should appear in skipped
             skipped = result.get("skills", {}).get("skipped", [])
-            self.assertTrue(
-                any("user-authored" in s for s in skipped),
-                f"Expected user-authored skip notice, got: {skipped}",
-            )
+            self.assertFalse(skipped, f"Did not expect copilot-instructions handling, got: {skipped}")
             # Marker IS created even when copilot-instructions.md is user-authored,
             # because other Copilot outputs (prompts, shared skills) are still managed.
             marker = root / ".github" / ".cf-installed"
@@ -2324,12 +2290,12 @@ def test_legacy_windsurf_non_cypilot_not_detected(self):
             self.assertFalse(_is_agent_installed("windsurf", root))
 
     def test_legacy_copilot_fallback_detection(self):
-        """Shared _is_agent_installed has legacy Copilot fallback via Constructor Studio-managed copilot-instructions.md."""
+        """Shared _is_agent_installed must no longer rely on copilot-instructions.md."""
         import importlib
         src = importlib.util.find_spec("studio.commands.agents").origin
         source = Path(src).read_text(encoding="utf-8")
-        self.assertIn("legacy_ci", source)
-        self.assertIn('startswith("# Constructor Studio")', source)
+        self.assertNotIn("legacy_ci", source)
+        self.assertNotIn('startswith("# Constructor Studio")', source)
 
     def test_openai_legacy_requires_codex_agents_content(self):
         """Shared _is_agent_installed requires .codex/agents/ with content, not bare .codex/ directory."""
diff --git a/tests/test_cli_integration.py b/tests/test_cli_integration.py
index ec932765..c49a1138 100644
--- a/tests/test_cli_integration.py
+++ b/tests/test_cli_integration.py
@@ -1471,7 +1471,6 @@ def test_all_agents_use_at_path(self):
             ],
             "copilot": [
                 ".agents/skills/cf/SKILL.md",
-                ".github/copilot-instructions.md",
                 ".github/prompts/cf.prompt.md",
             ],
             "cursor": [
diff --git a/tests/test_init_update_footprint.py b/tests/test_init_update_footprint.py
index 31a76164..a6d4d73a 100644
--- a/tests/test_init_update_footprint.py
+++ b/tests/test_init_update_footprint.py
@@ -186,7 +186,8 @@ def fake_install_default_kit(studio_dir, _interactive, _actions, _errors):
         assert ".bootstrap/config/kits/sdlc/" in gitignore
         assert ".bootstrap/config/kits/\n" not in gitignore
         assert ".github/\n" not in gitignore
-        assert ".github/prompts/cf*.prompt.md" in gitignore
+        assert ".github/prompts/cf.prompt.md" in gitignore
+        assert ".github/copilot-instructions.md" not in gitignore
         core = (root / ".bootstrap" / "config" / "core.toml").read_text(encoding="utf-8")
         assert 'tracking = "ignored"' in core
         assert (root / ".bootstrap" / "whatsnew.toml").is_file()
@@ -226,8 +227,8 @@ def test_init_tracked_runtime_and_agents_are_not_gitignored():
         gitignore = (root / ".gitignore").read_text(encoding="utf-8")
         assert ".bootstrap/.core/" not in gitignore
         assert ".bootstrap/.gen/" not in gitignore
-        assert ".codex/agents/cf*.toml" not in gitignore
-        assert ".github/prompts/cf*.prompt.md" not in gitignore
+        assert ".codex/.cf-installed" not in gitignore
+        assert ".github/prompts/cf.prompt.md" not in gitignore
         core = (root / ".bootstrap" / "config" / "core.toml").read_text(encoding="utf-8")
         assert 'runtime_tracking = "tracked"' in core
         assert 'agent_tracking = "tracked"' in core
diff --git a/tests/test_kit.py b/tests/test_kit.py
index f4b09a39..11ab372d 100644
--- a/tests/test_kit.py
+++ b/tests/test_kit.py
@@ -5092,57 +5092,7 @@ def test_existing_dir_overwritten(self):
             self.assertFalse((dst / "artifacts" / "PRD" / "old.md").exists())
 
 
-# ---------------------------------------------------------------------------
-# _collect_kit_metadata OSError
-# ---------------------------------------------------------------------------
-
-class TestCollectKitMetadataOsError(unittest.TestCase):
-    def test_agents_read_oserror(self):
-        from studio.commands.kit import _collect_kit_metadata
-        with TemporaryDirectory() as td:
-            kit_dir = Path(td) / "sdlc"
-            kit_dir.mkdir()
-            agents = kit_dir / "AGENTS.md"
-            agents.mkdir()  # directory, not file — read will fail
-            meta = _collect_kit_metadata(kit_dir, "sdlc")
-            self.assertEqual(meta["agents_content"], "")
-
-    def test_skill_nav_ignores_registered_custom_path(self):
-        from studio.commands.kit import _collect_kit_metadata
-        with TemporaryDirectory() as td:
-            kit_dir = Path(td) / "custom-kits" / "sdlc"
-            kit_dir.mkdir(parents=True)
-            (kit_dir / "SKILL.md").write_text("# Skill\n", encoding="utf-8")
-            meta = _collect_kit_metadata(kit_dir, "sdlc", "custom-kits/sdlc")
-            self.assertEqual(meta["skill_nav"], "")
-
-    def test_skill_nav_ignores_absolute_registered_custom_path(self):
-        from studio.commands.kit import _collect_kit_metadata
-        with TemporaryDirectory() as td:
-            kit_dir = Path(td) / "custom-kits" / "sdlc"
-            kit_dir.mkdir(parents=True)
-            (kit_dir / "SKILL.md").write_text("# Skill\n", encoding="utf-8")
-            meta = _collect_kit_metadata(kit_dir, "sdlc", kit_dir.as_posix())
-            self.assertEqual(meta["skill_nav"], "")
-
-    def test_skill_nav_ignores_windows_drive_registered_custom_path(self):
-        from studio.commands.kit import _collect_kit_metadata
-        with TemporaryDirectory() as td:
-            kit_dir = Path(td) / "custom-kits" / "sdlc"
-            kit_dir.mkdir(parents=True)
-            (kit_dir / "SKILL.md").write_text("# Skill\n", encoding="utf-8")
-            meta = _collect_kit_metadata(kit_dir, "sdlc", "C:/external-kits/sdlc")
-            self.assertEqual(meta["skill_nav"], "")
-
-    def test_skill_nav_ignores_windows_backslash_registered_custom_path(self):
-        from studio.commands.kit import _collect_kit_metadata
-        with TemporaryDirectory() as td:
-            kit_dir = Path(td) / "custom-kits" / "sdlc"
-            kit_dir.mkdir(parents=True)
-            (kit_dir / "SKILL.md").write_text("# Skill\n", encoding="utf-8")
-            meta = _collect_kit_metadata(kit_dir, "sdlc", r"C:\external-kits\sdlc")
-            self.assertEqual(meta["skill_nav"], "")
-
+class TestCollectRegisteredKitMetadata(unittest.TestCase):
     def test_registered_resource_metadata_uses_public_bindings_only(self):
         from studio.commands.kit import _collect_registered_kit_metadata
 
@@ -5824,7 +5774,7 @@ def test_ignores_unregistered_config_kit_dirs(self):
             self.assertFalse((adapter / ".gen" / "SKILL.md").exists())
             self.assertNotIn("# Loose Agents", gen_agents)
 
-    def test_uses_default_installed_kit_path_when_path_not_explicitly_registered(self):
+    def test_skips_default_installed_kit_path_when_resources_not_registered(self):
         from studio.commands.kit import regenerate_gen_aggregates
         from studio.utils import toml_utils
         with TemporaryDirectory() as td:
@@ -5852,7 +5802,7 @@ def test_uses_default_installed_kit_path_when_path_not_explicitly_registered(sel
 
             gen_agents = (adapter / ".gen" / "AGENTS.md").read_text(encoding="utf-8")
             self.assertFalse((adapter / ".gen" / "SKILL.md").exists())
-            self.assertIn("# Default Agents", gen_agents)
+            self.assertNotIn("# Default Agents", gen_agents)
 
     def test_deletes_legacy_generated_skill_aggregate(self):
         from studio.commands.kit import regenerate_gen_aggregates
@@ -5876,7 +5826,7 @@ def test_deletes_legacy_generated_skill_aggregate(self):
             self.assertEqual(result["gen_skill"], "deleted")
             self.assertFalse(legacy_skill.exists())
 
-    def test_uses_registered_custom_kit_path(self):
+    def test_skips_registered_custom_kit_path_when_resources_not_registered(self):
         from studio.commands.kit import regenerate_gen_aggregates
         from studio.utils import toml_utils
         with TemporaryDirectory() as td:
@@ -5905,9 +5855,9 @@ def test_uses_registered_custom_kit_path(self):
 
             gen_agents = (adapter / ".gen" / "AGENTS.md").read_text(encoding="utf-8")
             self.assertFalse((adapter / ".gen" / "SKILL.md").exists())
-            self.assertIn("# Custom Agents", gen_agents)
+            self.assertNotIn("# Custom Agents", gen_agents)
 
-    def test_uses_registered_absolute_custom_kit_path(self):
+    def test_skips_registered_absolute_custom_kit_path_when_resources_not_registered(self):
         from studio.commands.kit import regenerate_gen_aggregates
         from studio.utils import toml_utils
         with TemporaryDirectory() as td:
@@ -5936,7 +5886,7 @@ def test_uses_registered_absolute_custom_kit_path(self):
 
             gen_agents = (adapter / ".gen" / "AGENTS.md").read_text(encoding="utf-8")
             self.assertFalse((adapter / ".gen" / "SKILL.md").exists())
-            self.assertIn("# Custom Agents", gen_agents)
+            self.assertNotIn("# Custom Agents", gen_agents)
 
     def test_uses_registered_windows_drive_custom_kit_path(self):
         from studio.commands.kit import regenerate_gen_aggregates
diff --git a/tests/test_kit_manifest_install.py b/tests/test_kit_manifest_install.py
index 2bbe40a7..fe78af7f 100644
--- a/tests/test_kit_manifest_install.py
+++ b/tests/test_kit_manifest_install.py
@@ -281,6 +281,46 @@ def test_sync_manifest_resource_bindings_preserves_artifact_bindings(self):
         )
         self.assertNotIn("artifacts", merged["feature-template"])
 
+    def test_sync_manifest_resource_bindings_drops_removed_resources(self):
+        from studio.commands.kit import _sync_manifest_resource_bindings
+        from studio.utils import toml_utils
+
+        with TemporaryDirectory() as td:
+            config = Path(td) / "config"
+            config.mkdir()
+            toml_utils.dump({
+                "version": "1.0",
+                "project_root": "..",
+                "kits": {
+                    "mykit": {
+                        "format": "CFS",
+                        "path": "config/kits/mykit",
+                        "resources": {
+                            "skill": {"path": "config/kits/mykit/SKILL.md"},
+                            "stale": {"path": "config/kits/mykit/stale.md"},
+                        },
+                    },
+                },
+            }, config / "core.toml")
+            manifest = SimpleNamespace(
+                root="{cf-studio-path}/config/kits/{slug}",
+                resources=[
+                    SimpleNamespace(
+                        id="skill",
+                        kind="skill",
+                        install_path="SKILL.md",
+                        default_path="SKILL.md",
+                        public=False,
+                        artifact_bindings={},
+                    ),
+                ],
+            )
+
+            merged = _sync_manifest_resource_bindings(manifest, config, "mykit")
+
+        assert merged is not None
+        self.assertEqual(set(merged.keys()), {"skill"})
+
     def test_manifest_resource_bindings_writer_persists_artifact_bindings(self):
         from studio.commands.kit import _manifest_resource_bindings
 
diff --git a/tests/test_update.py b/tests/test_update.py
index d7d68aa7..205a8c47 100644
--- a/tests/test_update.py
+++ b/tests/test_update.py
@@ -1966,8 +1966,8 @@ def test_copilot_detected_via_cypilot_installed_marker(self):
             )
             self.assertIn("copilot", result)
 
-    def test_legacy_copilot_detected_via_managed_instructions(self):
-        """Legacy Copilot install detected via Constructor Studio-managed copilot-instructions.md."""
+    def test_legacy_copilot_instructions_do_not_trigger_detection(self):
+        """Legacy copilot-instructions.md alone must not trigger Copilot detection."""
         from studio.commands.update import _maybe_regenerate_agents
         with TemporaryDirectory() as td:
             root = Path(td) / "proj"
@@ -1984,7 +1984,7 @@ def test_legacy_copilot_detected_via_managed_instructions(self):
             result = _maybe_regenerate_agents(
                 {"skills": "updated"}, {}, root, cypilot_dir,
             )
-            self.assertIn("copilot", result)
+            self.assertNotIn("copilot", result)
 
     def test_user_copilot_instructions_does_not_trigger_detection(self):
         """User-authored .github/copilot-instructions.md must NOT trigger Copilot detection."""